bb_blast_best_hit - ampinzonv/BB3 GitHub Wiki

Function: bb_blast_best_hit

Extract the best BLAST hit per (qseqid, sseqid) pair from a tabular BLAST output.

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🔍 Description

This function parses a BLAST output file (in outfmt 6 with 14 columns) and retains only the best hit for each unique (query, subject) pair. The best hit is determined by the lowest e-value; if multiple hits share the same e-value, the one with the highest bitscore is selected.

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📥 Input

• A BLAST result file in tabular format (outfmt 6) with 14 columns.
• Use --input - for STDIN.

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📤 Output

• One line per unique (qseqid, sseqid) pair, representing the best hit.

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🧪 Examples

Filter best hits from a file:

bb_blast_best_hit --input blast_results.tsv

Using a pipeline:

cat blast_results.tsv | bb_blast_best_hit --input -

Save output:

bb_blast_best_hit --input blast_results.tsv --outfile best_hits.tsv

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⚙️ Usage

bb_blast_best_hit --input FILE [--outfile FILE] [--quiet] [--force]

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🧵 Options

Option	Description
--input FILE	Input BLAST file (outfmt 6, 14 columns) or - for STDIN (required)
--outfile FILE	Output file (optional, default: STDOUT)
--quiet	Suppress log messages
--force	Overwrite output file if it exists

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📌 Notes

• Input must include the following 14 columns:
  qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen
• If no valid hits are found or input is malformed, the function will return an error.